5b55

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'''Unreleased structure'''
 
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The entry 5b55 is ON HOLD until Paper Publication
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==Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form==
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<StructureSection load='5b55' size='340' side='right'caption='[[5b55]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5b55]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusobacterium_nucleatum_subsp._nucleatum_ATCC_25586 Fusobacterium nucleatum subsp. nucleatum ATCC 25586]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B55 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B55 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.14&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0JO:2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOIC+ACID'>0JO</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5b55 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b55 OCA], [https://pdbe.org/5b55 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b55 RCSB], [https://www.ebi.ac.uk/pdbsum/5b55 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b55 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8REP3_FUSNN Q8REP3_FUSNN]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Hydrogen sulfide (H2S) plays important roles in the pathogenesis of periodontitis. Oral pathogens typically produce H2S from L-cysteine in addition to pyruvate and NH4(+) However, fn1055 from Fusobacterium nucleatum subsp. nucleatum ATCC 25586 encodes a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the production of H2S and L-serine from L-cysteine and H2O, an unusual cysteine (hydroxyl) lyase reaction (beta-replacement reaction). To reveal the reaction mechanism, the crystal structure of substrate-free Fn1055 was determined. Based on this structure, a model of the L-cysteine-PLP Schiff base suggested that the thiol group forms hydrogen bonds with Asp(232) and Ser(74), and the substrate alpha-carboxylate interacts with Thr(73) and Gln(147) Asp(232) is a unique residue to Fn1055 and its substitution to asparagine (D232N) resulted in almost complete loss of beta-replacement activity. The D232N structure obtained in the presence of L-cysteine contained the alpha-aminoacrylate-PLP Schiff base in the active site, indicating that Asp(232) is essential for the addition of water to the alpha-aminoacrylate to produce the L-serine-PLP Schiff base. Rapid scan stopped-flow kinetic analyses showed an accumulation of the alpha-aminoacrylate intermediate during the reaction cycle, suggesting that water addition mediated by Asp(232) is the rate-limiting step. In contrast, mutants containing substitutions of other active-site residues (Ser(74), Thr(73), and Gln(147)) exhibited reduced beta-replacement activity by more than 100-fold. Finally, based on the structural and biochemical analyses, we propose a mechanism of the cysteine (hydroxyl) lyase reaction by Fn1055. This study leads to elucidation of the H2S-producing mechanism in F. nucleatum.
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Authors: Kezuka, Y., Yoshida, Y., Nonaka, T.
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Structural insights into the catalytic mechanism of cysteine (hydroxyl) lyase from the hydrogen-sulfide producing oral pathogen, Fusobacterium nucleatum.,Kezuka Y, Ishida T, Yoshida Y, Nonaka T Biochem J. 2018 Jan 17. pii: BCJ20170838. doi: 10.1042/BCJ20170838. PMID:29343611<ref>PMID:29343611</ref>
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Description: Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Kezuka, Y]]
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<div class="pdbe-citations 5b55" style="background-color:#fffaf0;"></div>
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[[Category: Yoshida, Y]]
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== References ==
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[[Category: Nonaka, T]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Fusobacterium nucleatum subsp. nucleatum ATCC 25586]]
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[[Category: Large Structures]]
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[[Category: Kezuka Y]]
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[[Category: Nonaka T]]
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[[Category: Yoshida Y]]

Current revision

Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form

PDB ID 5b55

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